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The measurement of discharge is fundamental in nutrient load estimation. Because of our ability to monitor discharge routinely, it is generally assumed that the associated uncertainty is low. This paper challenges this preconception, arguing that discharge uncertainty should be explicitly taken into account to produce robust statistical analyses. In many studies, paired discharge and chemical datasets are used to calculate ‘true’ loads and used as the benchmark to compare with other load estimates. This paper uses two years of high frequency (daily and sub-hourly) discharge and nutrient concentration data (nitrate-N and total phosphorus (TP)) collected at four field sites as part of the Hampshire Avon Demonstration Test Catchment (DTC) programme. A framework for estimating observational nutrient load uncertainty was used which combined a flexible non-parametric approach to characterising discharge uncertainty, with error modelling that allowed the incorporation of errors which were heteroscedastic and temporally correlated. The results showed that the stage–discharge relationships were non-stationary, and observational uncertainties from ±2 to 25% were recorded when the velocity–area method was used. The variability in nutrient load estimates ranged from 1.1 to 9.9% for nitrate-N and from 3.3 to 10% for TP when daily laboratory data were used, rising to a maximum of 9% for nitrate-N and 83% for TP when the sensor data were used. However, the sensor data provided a better representation of the ‘true’ load as storm events are better represented temporally, posing the question: is it more beneficial to have high frequency, lower precision data or lower frequency but higher precision data streams to estimate nutrient flux responses in headwater catchments? Copyright © 2015 John Wiley & Sons, Ltd.